Question: TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene name into common gene name
0
gravatar for salvocomplicazioni1
2.3 years ago by
salvocomplicazioni10 wrote:

I'm trying to analyze TCGA RNA-seq data, so i used TCGAbiolinks, I arrived at normalization data step and i obtained normalized counts matrix, How can I change Ensemble gene name into common gene name?

annotation grch38 tcgabiolinks • 1.0k views
ADD COMMENTlink modified 2.2 years ago by tiagochst150 • written 2.3 years ago by salvocomplicazioni10
Answer: TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene
2
gravatar for biomiha
2.3 years ago by
biomiha20
UK/Cambridge
biomiha20 wrote:

I would use biomaRt (https://bioconductor.org/packages/release/bioc/html/biomaRt.html)

ADD COMMENTlink written 2.3 years ago by biomiha20
Answer: TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene
2
gravatar for tiagochst
2.2 years ago by
tiagochst150
Brazil
tiagochst150 wrote:

You have the names inside the SummarizedExperiment object.

 

An example is in this gist:

 

For hg38 the gene names are retrieved with

values(data)$external_gene_name

 

For hg19 

values(data)$gene_id

 

Where data is the summarizedExperiment object, this data was created using biomaRt.

ADD COMMENTlink written 2.2 years ago by tiagochst150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 448 users visited in the last hour